The operational space formulation (Khatib, 1987), applied to rigid-body manipulators, describes how to decouple task-space and null-space dynamics, and write control equations that correspond only to forces at the end-effector or, alternatively, only to motion within the null-space. We would like to apply this useful theory to modern humanoids and other legged systems, for manipulation or similar tasks, however these systems present additional challenges due to their underactuated floating bases and contact states that can dynamically change. In recent work, Sentis et al. derived controllers for such systems by implementing a task Jacobian projected into a space consistent with the supporting constraints and underactuation (the so called "support consistent reduced Jacobian"). Here, we take a new approach to derive operational space controllers for constrained underactuated systems, by first considering the operational space dynamics within "projected inverse-dynamics" (Aghili, 2005), and subsequently resolving underactuation through the addition of dynamically consistent control torques. Doing so results in a simplified control solution compared with previous results, and importantly yields several new insights into the underlying problem of operational space control in constrained environments: 1) Underactuated systems, such as humanoid robots, cannot in general completely decouple task and null-space dynamics. However, 2) there may exist an infinite number of control solutions to realize desired task-space dynamics, and 3) these solutions involve the addition of dynamically consistent null-space motion or constraint forces (or combinations of both). In light of these findings, we present several possible control solutions, with varying optimization criteria, and highlight some of their practical consequences.

Personal robots can only become widespread if they are capable of safely operating among humans. In uncertain and highly dynamic environments such as human households, robots need to be able to instantly adapt their behavior to unforseen events. In this paper, we propose a general framework to achieve very contact-reactive motions for robotic grasping and manipulation. Associating stereotypical movements to particular tasks enables our system to use previous sensor experiences as a predictive model for subsequent task executions. We use dynamical systems, named Dynamic Movement Primitives (DMPs), to learn goal-directed behaviors from demonstration. We exploit their dynamic properties by coupling them with the measured and predicted sensor traces. This feedback loop allows for online adaptation of the movement plan. Our system can create a rich set of possible motions that account for external perturbations and perception uncertainty to generate truly robust behaviors. As an example, we present an application to grasping with the WAM robot arm.

We present an approach that enables robots to
learn motion primitives that are robust towards state estimation
uncertainties. During reaching and preshaping, the robot learns
to use fine manipulation strategies to maneuver the object into
a pose at which closing the hand to perform the grasp is more
likely to succeed. In contrast, common assumptions in grasp
planning and motion planning for reaching are that these tasks
can be performed independently, and that the robot has perfect
knowledge of the pose of the objects in the environment.
We implement our approach using Dynamic Movement
Primitives and the probabilistic model-free reinforcement learning
algorithm Policy Improvement with Path Integrals (PI2 ).
The cost function that PI2 optimizes is a simple boolean that
penalizes failed grasps. The key to acquiring robust motion
primitives is to sample the actual pose of the object from a
distribution that represents the state estimation uncertainty.
During learning, the robot will thus optimize the chance of
grasping an object from this distribution, rather than at one
specific pose.
In our empirical evaluation, we demonstrate how the motion
primitives become more robust when grasping simple cylindrical
objects, as well as more complex, non-convex objects. We
also investigate how well the learned motion primitives generalize
towards new object positions and other state estimation
uncertainty distributions.

{We consider projected Newton-type methods for solving large-scale optimization problems arising in machine learning and related fields. We first introduce an algorithmic framework for projected Newton-type methods by reviewing a canonical projected (quasi-)Newton method. This method, while conceptually pleasing, has a high computation cost per iteration. Thus, we discuss two variants that are more scalable, namely, two-metric projection and inexact projection methods. Finally, we show how to apply the Newton-type framework to handle non-smooth objectives. Examples are provided throughout the chapter to illustrate machine learning applications of our framework.}

Secondary metabolic pathway in plant is important for finding druggable candidate enzymes. However, there are many enzymes whose functions are still undiscovered especially in organism-specific metabolic pathways. We propose reaction graph kernels for automatically assigning the EC numbers to unknown enzymatic reactions in a metabolic network. Experiments are carried out on KEGG/REACTION database and our method successfully predicted the first three digits of the EC number with 83% accuracy.We also exhaustively predicted missing enzymatic functions in the plant secondary metabolism pathways, and evaluated our results in biochemical validity.

At the heart of many important bioinformatics problems, such as gene finding and function prediction, is the classification of biological sequences, above all of DNA and proteins. In many cases, the most accurate classifiers are obtained by training SVMs with complex sequence kernels, for instance for transcription starts or splice sites. However, an often criticized downside of SVMs with complex kernels is that it is very hard for humans to understand the learned decision rules and to derive biological insights from them. To close this gap, we introduce the concept of positional oligomer importance matrices (POIMs) and develop an efficient algorithm for their computation. We demonstrate how they overcome the limitations of sequence logos, and how they can be used to find relevant motifs for different biological phenomena in a straight-forward way. Note that the concept of POIMs is not limited to interpreting SVMs, but is applicable to general k&#8722;mer based scoring systems.

In recent years, spectral clustering has become one of the most popular modern clustering algorithms. It is simple to implement, can be solved efficiently by standard linear algebra software, and very often outperforms traditional clustering algorithms such as the k-means algorithm. On the first glance spectral clustering appears slightly mysterious, and it is not obvious to see why it works at all and what it really does. The goal of this tutorial is to give some intuition on those questions. We describe different graph Laplacians and their basic properties, present the most common spectral clustering algorithms, and derive those algorithms from scratch by several different approaches. Advantages and disadvantages of the different spectral clustering algorithms are discussed.

Protein subcellular localization is a crucial ingredient to many important inferences about cellular processes, including prediction of protein function and protein interactions.We propose a new class of protein sequence kernels which considers all motifs including motifs with gaps. This class of kernels allows the inclusion of pairwise amino acid distances into their computation. We utilize an extension of the multiclass support vector machine (SVM)method which directly solves protein subcellular localization without resorting to the common approach of splitting the problem into several binary classification problems. To automatically search over families of possible amino acid motifs, we optimize over multiple kernels at the same time. We compare our automated approach to four other predictors on three different datasets, and show that we perform better than the current state of the art. Furthermore, our method provides some insights as to which features are most useful for determining subcellular localization, which are in agreement with biological reasoning.

The abilities to learn and to categorize are fundamental for cognitive systems, be it animals or machines, and therefore have attracted attention from engineers and psychologists alike. Modern machine learning methods and psychological models of categorization are remarkably similar, partly because these two fields share a common history in artificial neural networks and reinforcement learning. However, machine learning is now an independent and mature field that has moved beyond psychologically or neurally inspired algorithms towards providing foundations for a theory of learning that is rooted in statistics and functional analysis. Much of this research is potentially interesting for psychological theories of learning and categorization but also hardly accessible for psychologists. Here, we provide a tutorial introduction to a popular class of machine learning tools, called kernel methods. These methods are closely related to perceptrons, radial-basis-function neural networks and exemplar theories of catego
rization. Recent theoretical advances in machine learning are closely tied to the idea that the similarity of patterns can be encapsulated in a positive definite kernel. Such a positive definite kernel can define a reproducing kernel Hilbert space which allows one to use powerful tools from functional analysis for the analysis of learning algorithms. We give basic explanations of some key conceptsthe so-called kernel trick, the representer theorem and regularizationwhich may open up the possibility that insights from machine learning can feed back into psychology.

Background: For splice site recognition, one has to solve two classification problems:
discriminating true from decoy splice sites for both acceptor and donor sites. Gene finding systems
typically rely on Markov Chains to solve these tasks.
Results: In this work we consider Support Vector Machines for splice site recognition. We employ
the so-called weighted degree kernel which turns out well suited for this task, as we will illustrate in
several experiments where we compare its prediction accuracy with that of recently proposed
systems. We apply our method to the genome-wide recognition of splice sites in Caenorhabditis
elegans, Drosophila melanogaster, Arabidopsis thaliana, Danio rerio, and Homo sapiens. Our
performance estimates indicate that splice sites can be recognized very accurately in these genomes
and that our method outperforms many other methods including Markov Chains, GeneSplicer and
SpliceMachine. We provide genome-wide predictions of splice sites and a stand-alone prediction
tool ready to be used for incorporation in a gene finder.
Availability: Data, splits, additional information on the model selection, the whole genome
predictions, as well as the stand-alone prediction tool are available for download at http://
www.fml.mpg.de/raetsch/projects/splice.

Invited keynote talk at the launch of BrainGain, the Dutch BCI research consortium, November 2007 (talk)

Abstract

I‘ll present a perspective on Brain-Computer Interface development from T{\"u}bingen. Some of the benefits promised by BCI technology lie in the near foreseeable future, and some further away. Our motivation is to make BCI technology feasible for the people who could benefit from what it has to offer soon: namely, people in the "completely locked-in" state. I‘ll mention some of the challenges of working with this user group, and explain the specific directions they have motivated us to take in developing experimental methods, algorithms, and software.

Compliant control will be a prerequisite for humanoid robotics if these robots are supposed to work safely and robustly in human and/or dynamic environments. One view of compliant control is that a robot should control a minimal number of degrees-of-freedom (DOFs) directly, i.e., those relevant DOFs for the task, and keep the remaining DOFs maximally compliant, usually in the null space of the task. This view naturally leads to task space control. However, surprisingly few implementations of task space control can be found in actual humanoid robots. This paper makes a first step towards assessing the usefulness of task space controllers for humanoids by investigating which choices of controllers are available and what inherent control characteristics they havethis treatment will concern position and orientation control, where the latter is based on a quaternion formulation. Empirical evaluations on an anthropomorphic Sarcos master arm illustrate the robustness of the different controllers as well as the eas
e of implementing and tuning them. Our extensive empirical results demonstrate that simpler task space controllers, e.g., classical resolved motion rate control or resolved acceleration control can be quite advantageous in face of inevitable modeling errors in model-based control, and that well chosen formulations are easy to implement and quite robust, such that they are useful for humanoids.

PET/MR combines the high soft tissue contrast of Magnetic Resonance Imaging (MRI) and the functional information of Positron Emission Tomography (PET). For quantitative PET information, correction of tissue photon attenuation is mandatory. Usually in conventional PET, the attenuation map is obtained from a transmission scan, which uses a rotating source, or from the CT scan in case of combined PET/CT. In the case of a PET/MR scanner, there is insufficient space for the rotating source and ideally one would want to calculate the attenuation map from the MR image instead. Since MR images provide information about proton density of the different tissue types, it is not trivial to use this data for PET attenuation correction. We present a method for predicting the PET attenuation map from a given the MR image, using a combination of atlas-registration and recognition of local patterns.
Using "leave one out cross validation" we show on a database of 16 MR-CT image pairs that our method reliably allows estimating the CT image from the MR image. Subsequently, as in PET/CT, the PET attenuation map can be predicted from the CT image. On an additional dataset of MR/CT/PET triplets we quantitatively validate that our approach allows PET quantification with an error that is smaller than what would be clinically significant.
We demonstrate our approach on T1-weighted human brain scans. However, the presented methods are more general and current research focuses on applying the established methods to human whole body PET/MRI applications.

Our goal is to understand the principles of Perception, Action and Learning in autonomous systems that successfully interact with complex environments and to use this understanding to design future systems